How to use the biotite.sequence.Location function in biotite

Check whether the high-level utility functions return the expected
    content of a known GenBank file. 
    """
    gb_file = gb.GenBankFile.read(join(data_dir("sequence"), "ec_bl21.gb"))
    assert gb.get_locus(gb_file) \
        == ("CP001509", 4558953, "DNA", True, "BCT", "16-FEB-2017")
    assert gb.get_definition(gb_file) \
        == ("Escherichia coli BL21(DE3), complete genome.")
    assert gb.get_version(gb_file) == "CP001509.3"
    assert gb.get_gi(gb_file) == 296142109
    assert gb.get_db_link(gb_file) \
        == {"BioProject" : "PRJNA20713", "BioSample" : "SAMN02603478"}
    annotation = gb.get_annotation(gb_file, include_only=["CDS"])
    feature = seq.Feature(
        "CDS",
        [seq.Location(5681, 6457, seq.Location.Strand.REVERSE)],
        {"gene": "yaaA", "transl_table": "11"}
    )
    in_annotation = False
    for f in annotation:
        if f.key == feature.key and f.locs == feature.locs and \
           all([(key, val in f.qual.items())
                for key, val in feature.qual.items()]):
                    in_annotation = True
    assert in_annotation
    assert len(gb.get_sequence(gb_file, format="gb")) == 4558953

def test_feature_without_id():
    """
    A feature without 'ID' should raise an error if it has multiple
    locations and consequently multiple entries in the GFF3 file.
    """
    annot = seq.Annotation(
        [seq.Feature(
            key  = "CDS",
            locs = [seq.Location(1,2), seq.Location(4,5)],
            qual = {"some" : "qualifiers"}
        )]
    )
    file = gff.GFFFile()
    with pytest.raises(ValueError):
        gff.set_annotation(file, annot)

def test_annotation_indexing():
    feature1 = Feature("CDS", [Location(-10,30 )], qual={"gene" : "test1"})
    feature2 = Feature("CDS", [Location(20, 50 )], qual={"gene" : "test2"})
    feature3 = Feature("CDS", [Location(100,130)], qual={"gene" : "test3"})
    feature4 = Feature("CDS", [Location(150,250)], qual={"gene" : "test4"})
    feature5 = Feature("CDS", [Location(-50,200)], qual={"gene" : "test5"})
    annotation = Annotation([feature1,feature2,feature3,feature4,feature5])
    sub_annot = annotation[40:150]
    # Only one location per feature
    assert set([list(f.locs)[0].defect for f in sub_annot]) \
        == set([Location.Defect.MISS_LEFT, Location.Defect.NONE,
                (Location.Defect.MISS_LEFT | Location.Defect.MISS_RIGHT)])
    assert set([f.qual["gene"] for f in sub_annot]) \
        == set(["test2", "test3", "test5"])

def test_annotation_creation():
    feature1 = Feature("CDS", [seq.Location(1,2)], qual={"gene" : "test1"})
    feature2 = Feature("CDS", [seq.Location(3,4)], qual={"gene" : "test2"})
    feature_list = [feature1, feature2]
    annotation = Annotation(feature_list)
    for feature in annotation:
        assert feature.key in [f.key for f in feature_list]
        assert feature.qual["gene"] in [
            f.qual["gene"] for f in feature_list
        ]

"""
Feature map of a synthetic operon
=================================

This script shows how to create a picture of an synthetic operon for
publication purposes.
"""

# Code source: Patrick Kunzmann
# License: BSD 3 clause

import matplotlib.pyplot as plt
from biotite.sequence import Annotation, Feature, Location
import biotite.sequence.graphics as graphics

strand = Location.Strand.FORWARD
prom  = Feature("regulatory", [Location(10, 50, strand)],
                {"regulatory_class" : "promoter",
                 "note"             : "T7"})
rbs1  = Feature("regulatory", [Location(60, 75, strand)],
                {"regulatory_class" : "ribosome_binding_site",
                 "note"             : "RBS1"})
gene1 = Feature("gene", [Location(81, 380, strand)],
                {"gene" : "gene1"})
rbs2  = Feature("regulatory", [Location(400, 415, strand)],
                {"regulatory_class" : "ribosome_binding_site",
                 "note"             : "RBS2"})
gene2 = Feature("gene", [Location(421, 1020, strand)],
                {"gene" : "gene2"})
term = Feature("regulatory", [Location(1050, 1080, strand)],
                {"regulatory_class" : "terminator"})
annotation = Annotation([prom, rbs1, gene1, rbs2, gene2, term])

# Code source: Patrick Kunzmann
# License: BSD 3 clause

import matplotlib.pyplot as plt
from biotite.sequence import Annotation, Feature, Location
import biotite.sequence.graphics as graphics

strand = Location.Strand.FORWARD
prom  = Feature("regulatory", [Location(10, 50, strand)],
                {"regulatory_class" : "promoter",
                 "note"             : "T7"})
rbs1  = Feature("regulatory", [Location(60, 75, strand)],
                {"regulatory_class" : "ribosome_binding_site",
                 "note"             : "RBS1"})
gene1 = Feature("gene", [Location(81, 380, strand)],
                {"gene" : "gene1"})
rbs2  = Feature("regulatory", [Location(400, 415, strand)],
                {"regulatory_class" : "ribosome_binding_site",
                 "note"             : "RBS2"})
gene2 = Feature("gene", [Location(421, 1020, strand)],
                {"gene" : "gene2"})
term = Feature("regulatory", [Location(1050, 1080, strand)],
                {"regulatory_class" : "terminator"})
annotation = Annotation([prom, rbs1, gene1, rbs2, gene2, term])

fig = plt.figure(figsize=(8.0, 0.8))
ax = fig.add_subplot(111)
graphics.plot_feature_map(
    ax, annotation, multi_line=False, loc_range=(1, 1101),
)
fig.tight_layout()

def _add_sec_str(annotation, first, last, str_type):
        if str_type == "a":
            str_type = "helix"
        elif str_type == "b":
            str_type = "sheet"
        else:
            # coil
            return
        feature = seq.Feature(
            "SecStr", [seq.Location(first, last)], {"sec_str_type" : str_type}
        )
        annotation.add_feature(feature)

# 'omit_oversized_labels' to False
    seq.Feature(
        "primer_bind",
        [seq.Location(1385, 1405)],
        {"note": "geneC"}
    ),
    seq.Feature(
        "primer_bind",
        [seq.Location(345, 365, seq.Location.Strand.REVERSE)],
        {"note": "geneC_R"}
    ),

    # Terminator
    seq.Feature(
        "regulatory",
        [seq.Location(310, 350)],
        {"regulatory_class": "terminator", "note": "MyTerm"}
    ),
])


fig = plt.figure(figsize=(8.0, 8.0))
ax = fig.add_subplot(111, projection="polar")
graphics.plot_plasmid_map(
    ax, annotation, plasmid_size=1500, label="My plasmid",
    label_properties={"fontsize": 8}
)

ticks = ax.get_xticks()
labels = ax.get_xticklabels()

fig.tight_layout()